Mapping is a prerequisite for most next generation sequencing
workflows and the SAM/BAM file format (1) is the de facto standard for
storing such large sequence alignments. BAMStats, is a
simple software tool built on the Picard Java API (2), which can
calculate and graphically display various metrics derived from SAM/BAM
files of value in QC assessments.
Implementation & availability
BAMStats is written in the Java programming language (Java 1.6) and
is available, both as pre-compiled executables, and as source code, from from the SourceForge download page. BAMstats is released as open source
software under the terms of the GNU General Public License.
Usage and system requirements
Two BAMstats jar executables providing command line (CLI) and graphic user (GUI) interfaces. For example, running the GUI with 6 GB of memory allocated:
java -Xmx6g -jar BAMStats-GUI-1.25.jar
Running the equivalent command line tool:
java -Xmx4g -jar BAMStats-1.25.jar -i <bam file>
BAMStats accepts sorted SAM or BAM files. A bed or gtf formatted
feature file, providing information on specific regions of interest
(e.g. exons, bait regions, etc.) can also be loaded alongside the
SAM/BAM file if required (Fig. 2).
BAMStats provides descriptive statistics for coverage, start
positions, MAPQ values, mapped read lengths and edit distances. Metrics
are given per reference sequence as described in the SAM/BAM file.
Metrics can also be generated for individual features such as exon or
bait region, if a suitable bed or gtf file is provided.